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An error occurred: basic_string::_M_replace_aux. #7
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The error fixed when I copy the actives1.pdbqt into the current directory. |
But another error occured when --gpu_batch was used and all the inputs were from Uni-Dock/example/screening_test/indata. INPUT: OUTPUT: If you used Uni-Dock in your work, please cite: Yu, Y., Cai, C., Wang, J., Bo, Z., Zhu, Z., & Zheng, H. (2023). Tang, S., Chen, R., Lin, M., Lin, Q., Zhu, Y., Ding, J., ... & Wu, J. (2022). J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli O. Trott, A. J. Olson, Please refer to https://github.com/dptech-corp/Uni-Dock/ for Scoring function : vina Computing Vina grid ... entering done ERROR: Empty ligand list. |
Please provide us the type and CUDA version of your GPU. It seems that global memory is less than required (about 8GB). BTW, |
Also, |
RTX3060 & CUDA11.4. Indeed, the global memory of the GPU influences the program. I reduced the number of ligands and used the --ligand_index option, and UniDock ran well. I also discovered that UniDock returns a 'segmentation fault (core dumped)' error if the grid size is too large. As for the 'ERROR: Empty ligand list.', it may also be due to the low memory of my laptop. |
Yes, we have hard constraints for grid size, which is 30A^3, and the largest length of either x, y or z is 48A. Please use 3090 or T4. We have tested Uni-Dock on these GPUs. |
INPUT:
unidock --receptor ./indata/def.pdbqt --ligand ./indata/def_unique_charged actives1.pdbqt --center_x -36.01 --center_y 25.63 --center_z 67.49 --size_x 22 --size_y 22 --size_z 22 --out ./result/ligand --exhaustiveness 128 --max_step 20 --num_modes 9 --scoring vina --refine_step 3 --seed 5 > ligand.log
OUTPUT:
Uni-Dock v0.1.0
If you used Uni-Dock in your work, please cite:
Yu, Y., Cai, C., Wang, J., Bo, Z., Zhu, Z., & Zheng, H. (2023).
Uni-Dock: GPU-Accelerated Docking Enables Ultralarge Virtual Screening.
Journal of Chemical Theory and Computation.
https://doi.org/10.1021/acs.jctc.2c01145
Tang, S., Chen, R., Lin, M., Lin, Q., Zhu, Y., Ding, J., ... & Wu, J. (2022).
Accelerating autodock vina with gpus. Molecules, 27(9), 3041.
DOI 10.3390/molecules27093041
J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force
Field, and Python Bindings, J. Chem. Inf. Model. (2021)
DOI 10.1021/acs.jcim.1c00203
O. Trott, A. J. Olson,
AutoDock Vina: improving the speed and accuracy of docking
with a new scoring function, efficient optimization and
multithreading, J. Comp. Chem. (2010)
DOI 10.1002/jcc.21334
Please refer to https://github.com/dptech-corp/Uni-Dock/ for
bug reporting, license agreements, and more information.
Scoring function : vina
Rigid receptor: ./indata/def.pdbqt
Ligands:
Grid center: X -36.01 Y 25.63 Z 67.49
Grid size : X 22 Y 22 Z 22
Grid space : 0.375
Exhaustiveness: 128
CPU: 0
Verbosity: 1
ERROR:
An error occurred: basic_string::_M_replace_aux.
Please report bugs through the Issue Tracker on GitHub
(https://github.com/dptech-corp/Uni-Dock/issues)., so
that this problem can be resolved. The reproducibility of the
error may be vital, so please remember to include the following in
your problem report:
Thank you!
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